We’re in a big warehouse surrounded by thousands of brown, cardboard boxes. You’d think you were in the back room of a shoe superstore. But these boxes contain the bones from an estimated 3,000 human skeletons, some of them more than 400 years old.

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They’re assembled at the Museum of London’s archaeology research centre, after being unearthed during excavation work for Crossrail, the new £15bn commuter railway line currently being built through London and the South East.

The bodies were buried in the Bethlem Burial Ground (also known as the New Churchyard), which opened in 1569 and was in continuous use until the 1730s. London’s first municipal graveyard, it provided the final resting place for thousands of Londoners.

And it has lain largely undisturbed under Liverpool Street – until the diggers arrived to carve out a new transport route for 21st-century Londoners.

Mike Henderson, senior human osteologist at the Museum of London, is currently in charge of the bones. It’s his job, working with the archaeologists, to find out as much as he can about the old skeletons before they’re reburied in a modern-day cemetery in Canvey Island.

But these bridge a fascinating gap – they will give us a real insight into the population in the 16th and 17th centuries and show us how London moved towards modern times.

A few of Henderson’s 3,000 skeletons will be subjected to scientific tests that could yield some modern-day benefits. Why?

Because Henderson is certain that the graveyard contains victims of the Great Plague of 1665 that killed more than 75,000 people – around a quarter of London’s population.

By comparing the DNA of the 17th-century plague victims with that of victims from other excavations who died 300 year earlier, scientists hope to discover how the bacteria, Yersinia Pestis, mutated over time.

That knowledge, says Henderson, could reveal how “plague was passed from person to person. If we know that, we might be able to better respond to diseases in the future – and prevent them from taking hold.”

Jay Carver is Crossrail’s lead archaeologist and working alongside Henderson. Carver says that plague had been a regular visitor to these shores – and then it stopped. “1665 was the last outbreak of bubonic plague in London, but we’re not entirely sure why it suddenly disappears.”

The schoolroom theory – that the disease was spread by infected rats, who died in the Great Fire the next year – may or may not be true, but “this massive rat population has never been attested in the archaeological record.” The skeletons may – possibly – provide an answer.

Scrapings will be taken from tooth enamel and bones and the specimens will be sent to microbiologists and palaeontologists for analysis.

There’s plenty more to learn from the find. Burial documents reveal that people from all walks of life were buried in the cemetery. “It’s a really massive range – a great cross-section of London’s population of that time,” says Carver.

It’s already possible to see some interesting trends. There are, in some of the skulls, round holes etched through the side of the teeth – evidence of the new (and very upmarket) habit of tobacco smoking.

The hole would have been the effect of clenching a clay pipe to the mouth.

And there are early indications of a surprising number of deaths among teenager and people in their 20s. Was this, Carver wonders, the result of “migrant” workers arriving in the city from the countryside and succumbing to new bugs?

Some of the burial records also cast an interesting light on the way people thought about death. There are many burials of very young children where the cause of seat his recorded, rather mysteriously, as “teeth” – parents, unable to explain what killed their child, put it down to the fact that they were teething at the time.

From plague deaths to clay pipes, these bones can certainly talk.

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London’s Lost Graveyard: the Crossrail Discovery will be shown on Sunday 18th July at 8pm on Channel 4

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